From: Axel Kohlmeyer (
Date: Sun May 25 2008 - 11:20:56 CDT

On Sun, 25 May 2008, Dong Xu wrote:

dx> Hi All,
dx> I have a question about mass weighted rms fit in ptraj. It is said

ptraj is a tool bundled with amber. wouldn't it be better to
ask on the amber mailing list or contact the author(s) of the tool?

dx> mass weighted rms fit is recommended than not. What's the advantage to
dx> have mass weights in the alignment process, say, the selection atoms
dx> are backbone, CA, C, N, O?

you example does not make sense. if there are only small differences
in the mass (as between carbon, nitrogen and oxygen) there can only
be small differences in the fit from using mass-weighting or not.


dx> Thanks!
dx> Dong Xu

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.